Characterization of Leptazolines A–D, Polar Oxazolines from the Cyanobacterium <i>Leptolyngbya</i> sp., Reveals a Glitch with the “Willoughby–Hoye” Scripts for Calculating NMR Chemical Shifts

Neupane, Jayanti Bhandari; Neupane, Ram; Luo, Yuheng; Yoshida, Wesley Y.; Sun, Rui; Williams, Philip G.

doi:10.1021/acs.orglett.9b03216

Cited by 53 publications

(38 citation statements)

References 22 publications

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“…Constituent models may be run on different infrastructure than was originally intended, especially as issues around computational reproducibility are addressed ( Barba, 2019 ; Hutton et al, 2016 ). Identical code run under different computational environments may produce different results (see for example Bhandari Neupane et al, 2019 ). Such infrastructure may differ in physical or virtual architecture (e.g., laptop, supercomputer, or operating systems) or method of generating/interpreting code (e.g., different languages, compilers, package versions).…”

Section: Scale Issues To Considermentioning

confidence: 99%

Socio-technical scales in socio-environmental modeling: Managing a system-of-systems modeling approach

Iwanaga

Wang

Hamilton

et al. 2021

Environmental Modelling & Software

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System-of-systems approaches for integrated assessments have become prevalent in recent years. Such approaches integrate a variety of models from different disciplines and modeling paradigms to represent a socio-environmental (or social-ecological) system aiming to holistically inform policy and decision-making processes. Central to the system-of-systems approaches is the representation of systems in a multi-tier framework with nested scales. Current modeling paradigms, however, have disciplinary-specific lineage, leading to inconsistencies in the conceptualization and integration of socio-environmental systems. In this paper, a multidisciplinary team of researchers, from engineering, natural and social sciences, have come together to detail socio-technical practices and challenges that arise in the consideration of scale throughout the socio-environmental modeling process. We identify key paths forward, focused on explicit consideration of scale and uncertainty, strengthening interdisciplinary communication, and improvement of the documentation process. We call for a grand vision (and commensurate funding) for holistic system-of-systems research that engages researchers, stakeholders, and policy makers in a multi-tiered process for the co-creation of knowledge and solutions to major socio-environmental problems.

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Section: Scale Issues To Considermentioning

confidence: 99%

Socio-technical scales in socio-environmental modeling: Managing a system-of-systems modeling approach

Iwanaga

Wang

Hamilton

et al. 2021

Environmental Modelling & Software

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“…A series of polar oxazolines, named leptazolines A–D ( 52–55 ), were isolated from the culture media of a Leptolyngbya sp. ( Figure 16 ) [ 51 ]. Their planar structures were characterized by MS and NMR along with formation of acetate derivatives.…”

Section: Chemical Diversity Of the Secondary Metabolites Isolated mentioning

confidence: 99%

“…Interestingly, the calculations were found to vary as a function of the computer operating system (Ubuntu 16, Windows 10, MAC Mavericks, MAC Mojave). Biological assay showed that leptazoline B ( 53 ) modestly inhibited the growth of PANC-1 cells, with a GI 50 of 10 µM [ 51 ], whereas leptazoline A ( 52 ) with its aromatic chlorine atom did not show any significant activity to this cell line.…”

Section: Chemical Diversity Of the Secondary Metabolites Isolated mentioning

confidence: 99%

The Chemistry, Biochemistry and Pharmacology of Marine Natural Products from Leptolyngbya, a Chemically Endowed Genus of Cyanobacteria

Naman

Alexander

et al. 2020

Marine Drugs

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Leptolyngbya, a well-known genus of cyanobacteria, is found in various ecological habitats including marine, fresh water, swamps, and rice fields. Species of this genus are associated with many ecological phenomena such as nitrogen fixation, primary productivity through photosynthesis and algal blooms. As a result, there have been a number of investigations of the ecology, natural product chemistry, and biological characteristics of members of this genus. In general, the secondary metabolites of cyanobacteria are considered to be rich sources for drug discovery and development. In this review, the secondary metabolites reported in marine Leptolyngbya with their associated biological activities or interesting biosynthetic pathways are reviewed, and new insights and perspectives on their metabolic capacities are gained.

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“…Bugs can be caused by typos, code behaving in unexpected ways, or logical flaws in the construction of the code. Outside of epidemiology, bugs have been found in code that had been used by many researchers [6] and may lead to retractions [7]. Bugs have also been found in highly influential work; a paper that informed austerity policies globally was found to have a fatal computational mistake [8].…”

Section: Introductionmentioning

confidence: 99%

Responsible modelling: Unit testing for infectious disease epidemiology

Lucas¹,

Pollington²,

Davis³

et al. 2020

Preprint

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Infectious disease epidemiology is increasingly reliant on large-scale computation and inference. Models have guided health policy for epidemics including COVID- 19 and Ebola and endemic diseases such as malaria and tuberculosis. Yet a single coding bug may bias results, leading to incorrect conclusions and wrong actions that could cause avoidable harm. We are ethically obliged to ensure our code is as free of error as possible. Unit testing is a coding method to avoid such bugs, but unit testing is rarely used in epidemiology. We demonstrate through simple examples how unit testing can handle the particular quirks of infectious disease models.

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Characterization of Leptazolines A–D, Polar Oxazolines from the Cyanobacterium Leptolyngbya sp., Reveals a Glitch with the “Willoughby–Hoye” Scripts for Calculating NMR Chemical Shifts

Cited by 53 publications

References 22 publications

Socio-technical scales in socio-environmental modeling: Managing a system-of-systems modeling approach

Socio-technical scales in socio-environmental modeling: Managing a system-of-systems modeling approach

The Chemistry, Biochemistry and Pharmacology of Marine Natural Products from Leptolyngbya, a Chemically Endowed Genus of Cyanobacteria

Responsible modelling: Unit testing for infectious disease epidemiology

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